Go Tree Trimming

Question

[ewre]

HI,

GO is a database with a hierarchy structure. the upper level terms include the lower ones. I want to trim this tree at certain level to remove the redundancy. any tools to do this trimming process?

Answer 1

[Ben Sutherland]

Hi ewre,

If you want to remove redundancy between enriched terms in your output you could try the tool GO Trimming outlined in "GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets" http://www.biomedcentral.com/1756-0500/4/267

with software provided here (also linked in the article): http://lucy.ceh.uvic.ca/go_trimming/cbr_go_trimming.py

[wilfried.souleyreau]

Hi,

I would like to remove redundancy between enriched terms, but GO Trimming it's no longer working, the analysis starts and never ends. It might be because the database is too old ? Do you have a more recent database for Go Trimming ?

Thanks a lot, Regards, WS